8OGX

Beta-glucuronidase from Acidobacterium capsulatum in complex with inhibitor R3794


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VNY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.1 M LiSO4, 0.5 M AmSO4, 0.1 M Trissodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.4850.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.999α = 90
b = 44.658β = 97.46
c = 137.023γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1241.1599.80.9925.16.433997
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051000.99

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT241.1532297169899.750.196650.194190.24406RANDOM18.368
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.760.642.1-1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.38
r_dihedral_angle_4_deg18.381
r_dihedral_angle_3_deg14.849
r_dihedral_angle_1_deg6.932
r_long_range_B_refined4.751
r_long_range_B_other4.461
r_scangle_other2.446
r_mcangle_it2.219
r_mcangle_other2.218
r_scbond_it1.675
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.38
r_dihedral_angle_4_deg18.381
r_dihedral_angle_3_deg14.849
r_dihedral_angle_1_deg6.932
r_long_range_B_refined4.751
r_long_range_B_other4.461
r_scangle_other2.446
r_mcangle_it2.219
r_mcangle_other2.218
r_scbond_it1.675
r_scbond_other1.617
r_angle_refined_deg1.616
r_mcbond_it1.5
r_mcbond_other1.494
r_angle_other_deg1.374
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3450
Nucleic Acid Atoms
Solvent Atoms441
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing